data_AYD
# 
_chem_comp.id                                    AYD 
_chem_comp.name                                  
;4-{[(4'-AMINO-2'-METHYLPYRIMIDIN-5'-YL)METHYL]AMINO}PENT-3-ENYL DIPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H20 N4 O7 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-10-31 
_chem_comp.pdbx_modified_date                    2008-10-14 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        382.247 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AYD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1N0H 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
AYD "N1'"  "N1'"  N 0 1 Y N N 3.781  105.275 52.542 -5.114 -2.231 -1.181 "N1'"  AYD 1  
AYD "C2'"  "C2'"  C 0 1 Y N N 3.931  106.077 53.701 -5.580 -2.522 0.017  "C2'"  AYD 2  
AYD CM2    CM2    C 0 1 N N N 5.039  107.035 53.864 -6.065 -3.921 0.295  CM2    AYD 3  
AYD "N3'"  "N3'"  N 0 1 Y N N 3.017  105.977 54.737 -5.633 -1.623 0.979  "N3'"  AYD 4  
AYD "C4'"  "C4'"  C 0 1 Y N N 1.885  105.065 54.682 -5.208 -0.380 0.770  "C4'"  AYD 5  
AYD "N4'"  "N4'"  N 0 1 N N N 1.039  105.032 55.740 -5.265 0.563  1.784  "N4'"  AYD 6  
AYD "C5'"  "C5'"  C 0 1 Y N N 1.682  104.189 53.461 -4.714 -0.037 -0.490 "C5'"  AYD 7  
AYD "C6'"  "C6'"  C 0 1 Y N N 2.693  104.337 52.384 -4.677 -1.013 -1.467 "C6'"  AYD 8  
AYD "C7'"  "C7'"  C 0 1 N N N 0.483  103.187 53.336 -4.227 1.360  -0.775 "C7'"  AYD 9  
AYD N3     N3     N 0 1 N N N -0.009 102.378 54.563 -2.872 1.523  -0.242 N3     AYD 10 
AYD C5     C5     C 0 1 N N N 0.993  101.092 56.636 -1.030 2.915  0.176  C5     AYD 11 
AYD C4     C4     C 0 1 N N N 0.839  101.359 55.096 -2.211 2.736  -0.386 C4     AYD 12 
AYD CM4    CM4    C 0 1 N N N 1.609  100.508 54.136 -2.841 3.849  -1.183 CM4    AYD 13 
AYD C6     C6     C 0 1 N N N 1.842  100.062 57.370 -0.338 1.762  0.858  C6     AYD 14 
AYD C7     C7     C 0 1 N N N 2.877  98.880  57.166 1.068  1.596  0.278  C7     AYD 15 
AYD O7     O7     O 0 1 N N N 4.140  98.065  57.711 1.724  0.504  0.924  O7     AYD 16 
AYD PA     PA     P 0 1 N N R 5.122  97.978  58.844 3.190  0.387  0.269  PA     AYD 17 
AYD O1A    O1A    O 0 1 N N N 6.097  96.958  58.702 3.064  0.258  -1.200 O1A    AYD 18 
AYD O2A    O2A    O 0 1 N N N 5.827  99.149  58.996 4.042  1.707  0.621  O2A    AYD 19 
AYD O3A    O3A    O 0 1 N N N 4.358  97.620  60.160 3.940  -0.909 0.859  O3A    AYD 20 
AYD PB     PB     P 0 1 N N N 3.419  96.455  60.630 5.199  -1.196 -0.102 PB     AYD 21 
AYD O1B    O1B    O 0 1 N N N 2.090  96.940  60.360 5.901  0.076  -0.389 O1B    AYD 22 
AYD O2B    O2B    O 0 1 N N N 3.764  96.295  62.012 6.211  -2.214 0.627  O2B    AYD 23 
AYD O3B    O3B    O 0 1 N N N 3.881  95.329  59.800 4.684  -1.848 -1.481 O3B    AYD 24 
AYD HM21   1HM2   H 0 0 N N N 5.157  107.665 54.775 -5.238 -4.526 0.665  HM21   AYD 25 
AYD HM22   2HM2   H 0 0 N N N 5.992  106.475 53.716 -6.856 -3.889 1.045  HM22   AYD 26 
AYD HM23   3HM2   H 0 0 N N N 5.026  107.717 52.982 -6.454 -4.360 -0.624 HM23   AYD 27 
AYD "H4'1" "1H4'" H 0 0 N N N 0.245  104.392 55.701 -5.617 0.319  2.654  "H4'1" AYD 28 
AYD "H4'2" "2H4'" H 0 0 N N N 0.698  105.975 55.924 -4.953 1.467  1.623  "H4'2" AYD 29 
AYD "H6'"  "H6'"  H 0 1 N N N 2.635  103.743 51.456 -4.298 -0.786 -2.452 "H6'"  AYD 30 
AYD "H7'1" "1H7'" H 0 0 N N N -0.388 103.739 52.912 -4.893 2.081  -0.301 "H7'1" AYD 31 
AYD "H7'2" "2H7'" H 0 0 N N N 0.716  102.467 52.516 -4.217 1.529  -1.852 "H7'2" AYD 32 
AYD HN3    HN3    H 0 1 N N N -0.919 101.971 54.347 -2.437 0.784  0.211  HN3    AYD 33 
AYD H5     H5     H 0 1 N N N 0.407  101.734 57.314 -0.559 3.887  0.148  H5     AYD 34 
AYD HM41   1HM4   H 0 0 N N N 2.270  99.712  54.551 -2.180 4.715  -1.184 HM41   AYD 35 
AYD HM42   2HM4   H 0 0 N N N 0.901  100.048 53.407 -3.003 3.514  -2.208 HM42   AYD 36 
AYD HM43   3HM4   H 0 0 N N N 2.208  101.166 53.464 -3.796 4.121  -0.735 HM43   AYD 37 
AYD H61    1H6    H 0 1 N N N 2.415  100.721 58.062 -0.269 1.962  1.928  H61    AYD 38 
AYD H62    2H6    H 0 1 N N N 1.063  99.551  57.984 -0.909 0.848  0.695  H62    AYD 39 
AYD H71    1H7    H 0 1 N N N 2.161  98.035  57.035 0.999  1.397  -0.791 H71    AYD 40 
AYD H72    2H7    H 0 1 N N N 3.260  99.150  56.154 1.639  2.511  0.441  H72    AYD 41 
AYD H2A    H2A    H 0 1 N N N 6.448  99.094  59.712 4.100  1.754  1.585  H2A    AYD 42 
AYD H2B    H2B    H 0 1 N N N 3.195  95.589  62.296 6.949  -2.358 0.019  H2B    AYD 43 
AYD H3B    H3B    H 0 1 N N N 3.312  94.623  60.084 4.234  -2.672 -1.250 H3B    AYD 44 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
AYD "N1'" "C2'"  DOUB Y N 1  
AYD "N1'" "C6'"  SING Y N 2  
AYD "C2'" CM2    SING N N 3  
AYD "C2'" "N3'"  SING Y N 4  
AYD CM2   HM21   SING N N 5  
AYD CM2   HM22   SING N N 6  
AYD CM2   HM23   SING N N 7  
AYD "N3'" "C4'"  DOUB Y N 8  
AYD "C4'" "N4'"  SING N N 9  
AYD "C4'" "C5'"  SING Y N 10 
AYD "N4'" "H4'1" SING N N 11 
AYD "N4'" "H4'2" SING N N 12 
AYD "C5'" "C6'"  DOUB Y N 13 
AYD "C5'" "C7'"  SING N N 14 
AYD "C6'" "H6'"  SING N N 15 
AYD "C7'" N3     SING N N 16 
AYD "C7'" "H7'1" SING N N 17 
AYD "C7'" "H7'2" SING N N 18 
AYD N3    C4     SING N N 19 
AYD N3    HN3    SING N N 20 
AYD C5    C4     DOUB N E 21 
AYD C5    C6     SING N N 22 
AYD C5    H5     SING N N 23 
AYD C4    CM4    SING N N 24 
AYD CM4   HM41   SING N N 25 
AYD CM4   HM42   SING N N 26 
AYD CM4   HM43   SING N N 27 
AYD C6    C7     SING N N 28 
AYD C6    H61    SING N N 29 
AYD C6    H62    SING N N 30 
AYD C7    O7     SING N N 31 
AYD C7    H71    SING N N 32 
AYD C7    H72    SING N N 33 
AYD O7    PA     SING N N 34 
AYD PA    O1A    DOUB N N 35 
AYD PA    O2A    SING N N 36 
AYD PA    O3A    SING N N 37 
AYD O2A   H2A    SING N N 38 
AYD O3A   PB     SING N N 39 
AYD PB    O1B    DOUB N N 40 
AYD PB    O2B    SING N N 41 
AYD PB    O3B    SING N N 42 
AYD O2B   H2B    SING N N 43 
AYD O3B   H3B    SING N N 44 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
AYD SMILES           ACDLabs              10.04 O=P(O)(O)OP(=O)(O)OCC/C=C(/NCc1cnc(nc1N)C)C                                                                                                                                
AYD InChI            InChI                1.02b InChI=1/C11H20N4O7P2/c1-8(13-6-10-7-14-9(2)15-11(10)12)4-3-5-21-24(19,20)22-23(16,17)18/h4,7,13H,3,5-6H2,1-2H3,(H,19,20)(H2,12,14,15)(H2,16,17,18)/b8-4+/f/h16-17,19H,12H2 
AYD InChIKey         InChI                1.02b DPGNBHAKLFOOJK-ACJSFTFYDO                                                                                                                                                  
AYD SMILES_CANONICAL CACTVS               3.341 CC(\NCc1cnc(C)nc1N)=C/CCO[P@](O)(=O)O[P](O)(O)=O                                                                                                                           
AYD SMILES           CACTVS               3.341 CC(NCc1cnc(C)nc1N)=CCCO[P](O)(=O)O[P](O)(O)=O                                                                                                                              
AYD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O)/C                                                                                                                         
AYD SMILES           "OpenEye OEToolkits" 1.5.0 Cc1ncc(c(n1)N)CNC(=CCCOP(=O)(O)OP(=O)(O)O)C                                                                                                                                
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
AYD "SYSTEMATIC NAME" ACDLabs              10.04 "(3E)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}pent-3-en-1-yl trihydrogen diphosphate"   
AYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(E)-4-[(4-amino-2-methyl-pyrimidin-5-yl)methylamino]pent-3-enyl] phosphono hydrogen phosphate" 
# 
